Covid 19 Exploration Project

library(tidyverse)

## -- Attaching packages --------------------------------------- tidyverse 1.3.0 --

## v ggplot2 3.3.5     v purrr   0.3.4
## v tibble  3.1.0     v dplyr   1.0.5
## v tidyr   1.1.3     v stringr 1.4.0
## v readr   1.3.1     v forcats 0.5.1

## -- Conflicts ------------------------------------------ tidyverse_conflicts() --
## x dplyr::filter() masks stats::filter()
## x dplyr::lag()    masks stats::lag()

covid19 <- read_csv("data/covid19-daily-cases.csv")

## Parsed with column specification:
## cols(
##   country_region = col_character(),
##   date = col_date(format = ""),
##   confirmed = col_double()
## )

covid19

covid19 %>% 
  ggplot(aes(
    x = date, 
    y = confirmed, 
    colour = country_region)) +
  geom_line() +
  guides(colour = FALSE)

## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.

# Fit with log scale so it becomes normal

covid19 %>% 
  ggplot(aes(
    x = date, 
    y = log10(confirmed),
    colour = country_region)) +
  geom_line() +
  guides(colour = FALSE)

## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.

#change scale for log
covid19 %>% 
  ggplot(aes(
    x = date, 
    y = confirmed, 
    colour = country_region)) +
  geom_line() +
  guides(colour = FALSE) +
  scale_y_log10()

## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.

## Warning: Transformation introduced infinite values in continuous y-axis

# sorting the data by countries
covid19_rel <- covid19 %>% 
  group_by(country_region) %>% 
  mutate(days = as.numeric(date - min(date))) %>% 
  ungroup()
covid19_rel

#graph for countries and days since march 1
world <- covid19_rel %>% 
  ggplot(aes(
    x = days,
    y = confirmed, 
    colour = country_region)) +
  geom_line() +
  scale_y_log10() +
  guides(colour = FALSE)

## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.

world

## Warning: Transformation introduced infinite values in continuous y-axis

# nz highlighted out of all countries
covid19_nz <- covid19_rel %>% 
  filter(country_region == "New Zealand")
p_nz <- covid19_rel %>% 
  ggplot(aes(x = days, y = confirmed, 
    group = country_region)) +
  geom_line(colour = "grey", alpha = 0.5) +
  geom_line(colour = "#238b45", size = 1, data = covid19_nz) +
  scale_y_log10() +
  guides(colour = FALSE)

## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.

p_nz

## Warning: Transformation introduced infinite values in continuous y-axis

#changed labels
p_nz <- p_nz +
  geom_label(aes(
    x = max(days), y = max(confirmed),
    label = country_region), data = covid19_nz,
    colour = "#238b45", nudge_x = 3, nudge_y = .5)
p_nz

## Warning: Transformation introduced infinite values in continuous y-axis

p_nz <- p_nz +
  scale_y_log10(labels = scales::label_comma()) +
  xlim(c(0, 100))

## Scale for 'y' is already present. Adding another scale for 'y', which will
## replace the existing scale.

p_nz

## Warning: Transformation introduced infinite values in continuous y-axis

p_nz <- p_nz +
  labs(
    x = "Days since March 1",
    y = "Confirmed cases (on log10)",
    title = "Worldwide coronavirus confirmed cases",
    subtitle = "highlighting New Zealand",
    caption = "Data source: John Hopkins University, CSSE"
  )
p_nz

## Warning: Transformation introduced infinite values in continuous y-axis

#make interactive
library(plotly)

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
##     filter

## The following object is masked from 'package:graphics':
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##     layout

ggplotly(p_nz)

## Warning: Transformation introduced infinite values in continuous y-axis

## Warning in geom2trace.default(dots[[1L]][[1L]], dots[[2L]][[1L]], dots[[3L]][[1L]]): geom_GeomLabel() has yet to be implemented in plotly.
##   If you'd like to see this geom implemented,
##   Please open an issue with your example code at
##   https://github.com/ropensci/plotly/issues